The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index.
Ensembl comparative genomics resources
Open accessAbstract
Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,641
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,235
Identification of common molecular subsequences
Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,940
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Cited by
OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676
CADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1016 · Cited by 3,534
The Human Transcription Factors
Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399
Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1098 · Cited by 2,605
Self-citationYates, A. D., Achuthan, P., Akanni, W., Allen, J., Allen, J., Alvarez-Jarreta, J., Amode, M. R., Armean, I. M., Azov, A. G., Bennett, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz966 · Cited by 1,152
Self-citationCunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., Bennett, R., Bhai, J., Billis, K., Boddu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1113 · Cited by 925
Self-citationAken, B. L., Achuthan, P., Akanni, W., Amode, M. R., Bernsdorff, F., Bhai, J., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1104 · Cited by 512
Self-citationThe functional landscape of the human phosphoproteome
Ochoa, D., Jarnuczak, A. F., Viéitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A. A., Hill, A., Garcia-Alonso, L., Stein, F., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0344-3 · Cited by 491
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome
Wucher, V., Legeai, F., Hédan, B., Rizk, G., Lagoutte, L., Leeb, T., Jagannathan, V., Cadieu, E., David, A., Lohi, H., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1306 · Cited by 470
Schubach, M., Maass, T., Nazaretyan, L., Röner, S., & Kircher, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad989 · Cited by 455
Hunt, S. E., McLaren, W., Gil, L., Thormann, A., Schuilenburg, H., Sheppard, D., Parton, A., Armean, I. M., Trevanion, S. J., Flicek, P., et al. (2018) · Database · doi:10.1093/database/bay119 · Cited by 452
Self-citationThe landscape of sex-differential transcriptome and its consequent selection in human adults
Gershoni, M., & Pietrokovski, S. (2017) · BMC Biology · doi:10.1186/s12915-017-0352-z · Cited by 266
Progranulin, lysosomal regulation and neurodegenerative disease
Kao, A. W., McKay, A., Singh, P. P., Brunet, A., & Huang, E. J. (2017) · Nature Reviews Neuroscience · doi:10.1038/nrn.2017.36 · Cited by 258
Gene expression variability across cells and species shapes innate immunity
Hagai, T., Chen, X., Miragaia, R. J., Rostom, R., Gomes, T., Kunowska, N., Henriksson, J., Park, J.-E., Proserpio, V., Donati, G., et al. (2018) · Nature · doi:10.1038/s41586-018-0657-2 · Cited by 220
Inferring Orthology and Paralogy
Altenhoff, A. M., Glover, N. M., & Dessimoz, C. (2019) · Methods in Molecular Biology · doi:10.1007/978-1-4939-9074-0_5 · Cited by 148
Predicting functional effect of missense variants using graph attention neural networks
Zhang, H., Xu, M. S., Fan, X., Chung, W. K., & Shen, Y. (2022) · Nature Machine Intelligence · doi:10.1038/s42256-022-00561-w · Cited by 98
Parey, E., Louis, A., Montfort, J., Guiguen, Y., Crollius, H. R., & Berthelot, C. (2022) · Genome Research · doi:10.1101/gr.276953.122 · Cited by 83
Accurate detection of convergent amino-acid evolution with PCOC
Rey, C., Guéguen, L., Sémon, M., & Boussau, B. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy114 · Cited by 82
Paralog dependency indirectly affects the robustness of human cells
Dandage, R., & Landry, C. R. (2019) · Molecular Systems Biology · doi:10.15252/msb.20198871 · Cited by 65
Sharma, V., & Hiller, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx554 · Cited by 72
Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications
Parey, E., Louis, A., Cabau, C., Guiguen, Y., Roest Crollius, H., & Berthelot, C. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa149 · Cited by 49
Denisovan introgression has shaped the immune system of present-day Papuans
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46
Ten Years of Collaborative Progress in the Quest for Orthologs
Linard, B., Ebersberger, I., McGlynn, S. E., Glover, N., Mochizuki, T., Patricio, M., Lecompte, O., Nevers, Y., Thomas, P. D., Gabaldón, T., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab098 · Cited by 45
Self-citationKlug, N. R., Chechneva, O. V., Hung, B. Y., & O’Donnell, M. E. (2021) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00177.2019 · Cited by 21
Metadata
- Authors
- Herrero, J., Muffato, M., Beal, K., Fitzgerald, S., Gordon, L., Pignatelli, M., Vilella, A. J., Searle, S. M. J., Amode, R., Brent, S., Spooner, W., Kulesha, E., Yates, A., & Flicek, P.
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2016
- Volume
- 2016
- Pages
- bav096
- ISSN
- 1758-0463 (ISSN-L)
- OpenAlex
- W2281531600
- Cited by
- 434
- References
- 73
- FWCI
- 27.99
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
